Is CD151 c.456+20A>G pathogenic?

CD151 c.456+20A>G is classified Likely benign in CD151 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2025-06-11). Very rare (popmax 0.00246%, nfe).

How common is CD151 c.456+20A>G in the general population?

CD151 c.456+20A>G is very rare (popmax 0.00246%, nfe) (gnomAD).

CD151 c.456+20A>G

VCV3607284

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

very rare (popmax 0.00246%, nfe)

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
Splice region	donor +20	near-intronic (+20 nt from the splice site)
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -0.44	GERP -2.5
Overall
CADD	0.567	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00246% European (non-Finnish) · 29/1,178,062 alleles

Filtering AF 0.00173% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00149%

Overall 0.0018% 29/1,610,162 alleles · very rare

Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.

Variant & gene context

Gene: CD151
Coding: c.456+20A>G
MANE Select: NM_004357
Type: single nucleotide variant
Location: chr11:837374 (GRCh38)
Gene constraint: LOEUF 0.816 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 88.02

Full CD151 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CD151 p.Lys7Ter Pathogenic ★★ same type
CD151 c.352-11C>G Uncertain significance ★★ same type
CD151 c.702+4A>G Uncertain significance ★★ same type
CD151 c.702+5G>C Uncertain significance ★★ same type
CD151 p.Ala145Thr Uncertain significance ★★ ⚠ same type
CD151 p.Ala81Thr Uncertain significance ★★ ⚠ same type
CD151 p.Arg133Cys Uncertain significance ★★ ⚠ same type
CD151 p.Arg165Gln Uncertain significance ★★ ⚠ same type

Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →

Cite Sugi Variant

Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/cd151-c-456-plus-20a-g (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown